Hmmm… useful ideas here.
I think that I would go a bit further in respect of X/Y 0,0 position. I don’t really understand why the coordinates are not both known and configurable. It would enable the user to define the coordinates (relatively positioned) or work to the machine derived coordinates (absolutely positioned). Depending on the module fitted, the machine should always know where it is in cartesian space. I would also add that it should talk to the software (whatever is being used) and tell the software where the module is sitting in 3D space. I would wish for the display screen to provide a constant position readout, whether it was machine derived or user specified.
Run boundary is a completely unnecessary command. When you know the dimensions of the clamps and the intrusion of the clamp head into the workpiece space, there is no need to have or use a run boundary command. It is provided ostensibly to ensure that the machine tool will not hit the clamp or any other obstruction in the workspace. I know what size my clamps are and if I draw my boundary inside their 5mm intrusion zone and their height, the endmill bit will never hit them. I set my jog height to 1mm above the 5mm clamp height and 1mm inside the 5mm clamp and I know that the endmill bit will never run into the clamps. See this post: Modifying the SM1 Table and its Clamp System
The lack of an emergency stop (this should be an instant response to whatever operation is being completed and the user wants to stop) is a major flaw in the software and an unsafe practice. At the very least it should be supplied in software and backed up with a physical switch. Pause and resume are subordinate requirements… that any well thought out emergency stop function would provide. After a stop is initiated, all settings would be retained and continued from the stop point after the machine is restarted.